1543 harmonize description of time series infection states etc in documentation

[jubicker]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• Use `` in the documentation when refered to classes
• replace mio::TimeSeries just by TimeSeries

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closes #1543

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.40%. Comparing base (c83172c) to head (fb0ddb0).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

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##             main    #1545   +/-   ##
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  Coverage   97.40%   97.40%           
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  Files         190      190           
  Lines       16858    16866    +8     
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+ Hits        16420    16428    +8     
  Misses        438      438           

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[kilianvolmer]

Thank you for making all these changes! I found only a few things you overlooked. However, I suggest removing all the mentions of mio from TimeSeries as they were used very inconsistently.
Finally, I would actually prefer to use TimeSeries instead of :code:TimeSeries, for consistency and easy reading of the rst files. What do you think of that?

[jubicker]

Thank you! Removing mio:: from TimeSeries and using TimeSeries instead of the :code: version sounds good. I'll do that and rerequest your review once done :)

[kilianvolmer]

I found a couple more mentions to change.

[Copilot]

Pull request overview

This PR harmonizes documentation terminology and formatting around core modeling concepts (e.g., time series, infection states, model types) to consistently distinguish code objects from general prose, addressing #1543.

Changes:

• Replace bold/normal-text code-object references with inline code formatting (... / :code:...).
• Standardize references to TimeSeries by dropping mio:: in narrative text.
• Apply the same formatting harmonization across multiple Python and C++ documentation pages.

Reviewed changes

Copilot reviewed 31 out of 31 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
docs/source/python/m-simulation_model_usage.rst	Use inline code formatting for DynamicNPIs, TimeSeries, FlowModel in Python tutorial text.
docs/source/python/m-simulation_expanding_bindings.rst	Format TimeSeries as inline code in bindings tutorial.
docs/source/getting_started.rst	Format infection state / flow model references as inline code in getting started overview.
docs/source/cpp/temporal_hybrid.rst	Replace narrative mio::TimeSeries references with TimeSeries inline code.
docs/source/cpp/smm.rst	Replace bold code-object references with inline code formatting (e.g., Influence, Simulation, TimeSeries).
docs/source/cpp/sde.rst	Replace bold code-object references with inline code formatting (StochasticModel, CompartmentalModel, etc.).
docs/source/cpp/sbml.rst	Format Populations as inline code in SBML limitations text.
docs/source/cpp/performance_monitoring.rst	Consistently format timing framework class names (AutoTimer, BasicTimer, etc.) as inline code.
docs/source/cpp/ode_creation.rst	Format CompartmentalModel, FlowModel, Parameters, mio::AgeGroup references consistently.
docs/source/cpp/ode.rst	Replace bold code-object references with inline code formatting across ODE overview.
docs/source/cpp/models/osir.rst	Harmonize code-object formatting (InfectionState, CompartmentalModel, AgeGroup, Populations).
docs/source/cpp/models/oseirv.rst	Harmonize code-object formatting (InfectionState, FlowModel, AgeGroup, Populations, TimeSeries).
docs/source/cpp/models/oseirdb.rst	Harmonize code-object formatting (InfectionState, FlowModel, AgeGroup, Populations, TimeSeries).
docs/source/cpp/models/oseir.rst	Harmonize code-object formatting (InfectionState, FlowModel, AgeGroup, Populations, TimeSeries).
docs/source/cpp/models/osecirvvs.rst	Harmonize code-object formatting (InfectionState, FlowModel, Simulation, TimeSeries).
docs/source/cpp/models/osecirts.rst	Harmonize code-object formatting (InfectionState, FlowModel, AgeGroup, Populations, TimeSeries).
docs/source/cpp/models/osecir.rst	Harmonize code-object formatting (InfectionState, FlowModel, AgeGroup, Populations, DynamicNPIs, TimeSeries).
docs/source/cpp/models/omseirs4.rst	Harmonize code-object formatting (InfectionState, CompartmentalModel, TimeSeries).
docs/source/cpp/models/lsecir2d.rst	Replace narrative mio::TimeSeries mentions with TimeSeries and avoid code-styling generic “infection states”.
docs/source/cpp/models/lsecir.rst	Replace narrative mio::TimeSeries mentions with TimeSeries and avoid code-styling generic “infection states”.
docs/source/cpp/models/iseir.rst	Use inline code formatting for TimeSeries and InfectionState.
docs/source/cpp/models/isecir.rst	Use inline code formatting for InfectionState, Simulation, TimeSeries, InfectionTransition.
docs/source/cpp/models/glsecir.rst	Replace narrative mio::TimeSeries mentions with TimeSeries and avoid code-styling generic “infection states”.
docs/source/cpp/mobility_based_abm.rst	Format TimeSeries as inline code in ABM history description.
docs/source/cpp/lct_creation.rst	Format Parameters, mio::ParameterSet, CompartmentalModel, TimeSeries references as inline code.
docs/source/cpp/lct.rst	Harmonize code-object formatting (InfectionState, LctInfectionState, CompartmentalModel, TimeSeries, etc.).
docs/source/cpp/io.rst	Replace narrative mio::TimeSeries mentions with TimeSeries and format IO framework concept names as inline code.
docs/source/cpp/ide.rst	Harmonize code-object formatting and adjust where “time series” is used as a general concept vs code object.
docs/source/cpp/glct.rst	Harmonize code-object formatting for GLCT docs (InfectionState, LctInfectionState, etc.).
docs/source/cpp/diffusive_abm.rst	Harmonize code-object formatting (QuadWell, SingleWell, Influence, Simulation, TimeSeries).
docs/source/cpp/data_types.rst	Switch selected data type names (e.g., TimeSeries, ContactMatrix) to inline code formatting in the table.

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[kilianvolmer]

Thank you for changing all the inline code blocks! I found a few more things we should change but I hope then we have everything.

[kilianvolmer]

Great! I fixed the last problems, we are ready to merge! 🥳

[jubicker]

looks good :)